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dc.contributor.authorO'Sullivan, Daniel*
dc.date.accessioned2016-09-29T16:32:19Z
dc.date.available2016-09-29T16:32:19Z
dc.date.issued2015
dc.identifier.citationO'Sullivan, Daniel. The Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality Defects. 2015. Thesis, University College, Corken_GB
dc.identifier.urihttp://hdl.handle.net/11019/1074
dc.descriptionDoctoral thesisen_GB
dc.description.abstractHigh throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencingbased approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbeassociated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses.en_GB
dc.description.sponsorshipThanks to the Teagasc for the Walsh Fellowship and the Food Institutional Research Measure for funding my work.en_GB
dc.language.isoenen_GB
dc.subjectCheese qualityen_GB
dc.subjectHigh throughput next generation sequencingen_GB
dc.subjectmicrobial communities.en_GB
dc.subjectLycopeneen_GB
dc.subjectdefect-causing microbial populationsen_GB
dc.titleThe Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality Defectsen_GB
dc.typeThesisen_GB
dc.contributor.sponsorTeagasc Walsh Fellowship Programme
refterms.dateFOA2018-01-12T08:35:36Z


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